Coho, Jack Coho, and Steelhead in the Columbia River Basin
The Columbia River Basin watershed is home to several species of salmonids, inlcuding Sockeye, Coho, Jack Coho, Steelhead, and Wild Steelhead. Columbia River DART (Data Access in Real Time) provides comprehensive population and environmental data for 10 species in multiple survey locations in the basin over the last 100 years. In this report, we utilize the DART data to visualize population and adult passage trends for Coho, Jack Coho, and Steelhead across the Willamette Falls fish ladder.
# Read in data
fish_raw <- read_csv("willamette_fish_passage.csv")
# Make a subset with coho, steelhead, jack coho
fish_sub <- fish_raw %>%
clean_names() %>%
select(project, date, coho, jack_coho, steelhead)
# Create time series
fish_ts <- fish_sub %>%
mutate(date = mdy(date)) %>%
as_tsibble(key = NULL, index = date)
Columbia River Basin DART Adult Passage Graphics & Text | Columbia Basin Research. http://www.cbr.washington.edu/dart/query/adult_graph_text.
# Tab 1 - time series graph
# Replace na values with 0
fish_ts_na <- fish_ts %>%
replace(is.na(.), 0)
# Create ts graph, but in separate panels
ts_coho <- ggplot(data = fish_ts_na) +
geom_line(aes(x = date, y = coho), color = "deeppink2") +
labs(y = "Coho Count", x = "Year") +
theme_minimal() +
theme(axis.text.x = element_text(angle = 90))
ts_steelhead <- ggplot(data = fish_ts_na) +
geom_line(aes(x = date, y = steelhead), color = "goldenrod") +
labs(y = "Steelhead Count", x = "Year") +
theme_minimal() +
theme(axis.text.x = element_text(angle = 90))
ts_jack_coho <- ggplot(data = fish_ts_na) +
geom_line(aes(x = date, y = jack_coho), color = "blue2") +
labs(y = "Jack Coho Count", x = "Year") +
theme_minimal() +
theme(axis.text.x = element_text(angle = 90))
library(patchwork)
ts_coho | ts_steelhead | ts_jack_coho
Figure 1. Shows visual counts of Coho (pink),Steelhead (golden), and Jack Coho (blue) in adult passages in the Willamette Falls Columbia River DART survey location. Observations were taken daily from 2001 to 2010. Data source: Columbia Basin Research.
There appears to be seasonality for all three fish species (Coho, Steelhead, and Jack Coho).
Steelhead and Jack Coho counts remain relatively stable throughout the time period, whereas Coho counts increased and peaked toward the end of the time period.
# Create Seasonplot showing value (counts) for each day over entire span of data, store as object
final <- annual_fish %>%
gg_season(y = value) +
facet_wrap(~species, ncol = 1, scales = "free") %>%
labs(x = "Month", y = "Counts") +
theme_minimal()
final
Figure 2. shows visual counts of Coho, Jack Coho, and Steelhead in adult passages in the Willamette Falls Columbia River DART survey location. Observations were taken daily from 2001 to 2010. Data source: Columbia Basin Research.
On average, Coho and Jack Coho use the Willamette Falls fish passages only during the Fall months, while Steelhead seem to use them from the early spring into mid-summer.
The Coho population rapidly increases in later years (2009-2010), with peak annual visual counts in 2010 more than triple those in 2008. This upward trend is seen on smaller levels in the Jack Coho and Steelhead populations.
# Now let's plot this!
ggplot(data = annual_fish, aes(x = year, y = total, color = species)) +
geom_line() +
scale_color_manual(values=c("deeppink2", "blue2", "goldenrod")) +
geom_point(size = 2,
alpha = 0.8) +
scale_x_continuous(breaks = c(2000, 2002, 2004, 2006, 2008, 2010)) +
labs( x = "Year",
y = "Annual Fish Observations",
color = "Species") +
theme_minimal()
Figure 3. Shows counts of Coho (pink),Steelhead (golden), and Jack Coho (blue), totaled annually, from the Willamette Falls observation site. Data source: Columbia Basin Research.